Mitochondrial Disease Genetic Diagnostics

ABSTRACT

Mitochondrial disease genetic diagnostics and methods of use thereof.

This application is a continuation application of U.S. patent application Ser. No. 15/032,520, filed Apr. 27, 2016, which is a § 371 application of PCT/US2014/063449, filed Oct. 31, 2014, which claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application No. 61/898,171, filed on Oct. 31, 2013. The foregoing applications are incorporated by reference herein.

This invention was made with government support under Grant No. R03-DK082446 awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to the field of mitochondrial diseases. Specifically, the instant invention provides compositions and methods for the diagnosis of mitochondrial diseases.

BACKGROUND OF THE INVENTION

Several publications and patent documents are cited throughout the specification in order to describe the state of the art to which this invention pertains. Each of these citations is incorporated herein by reference as though set forth in full.

Whole-exome sequencing (WES) has emerged as the preferred method to identify disease genes for Mendelian disorders. Indeed, WES is proving particularly valuable for the diagnostic evaluation of individuals with phenotypically and genetically heterogeneous conditions such as suspected mitochondrial disease (McCormick et al. (2013) Neurotherapeutics 10:251-61). Mitochondrial diseases have a wide range of presenting disease manifestations, typically poor genotype-phenotype correlation of any one gene, and a wide range of phenotypically similar non-mitochondrial diseases that must be considered in the differential diagnosis for any given patient (Haas et al. (2007) Pediatrics 120:1326-1333). Known pathogenic mutations causing mitochondrial disease have already been identified in more than 150 nuclear genes and all 37 mtDNA genes (Calvo et al. (2010) Annu. Rev. Genomics Hum. Genet., 11:25-44), although most genes have been linked to only a small number of disease cases and mutations in these known genes collectively account for less than half of cases with suspected mitochondrial disease (Calvo et al. (2012) Sci. Transl. 4:118ra110). Additional pathogenic candidates abound as there are up to 1,500 mitochondrial proteins that are largely nuclear-encoded, of which the MitoCarta set of 1,034 proteins has undergone robust experimental validation and accounts for approximately 85% of all mitochondrial proteins (Pagliarini et al. (2008) Cell 134:112-123). The MitoCarta set includes many known disease genes, including all but 4 nuclear genes (TAZ, PUS1, RRM2B, TYMP) of 77 (Calvo et al. (2012) Sci. Transl. Med., 4:118ra110) previously linked to mitochondrial respiratory chain disease (Tucker et al. (2010) Curr. Neurol. Neurosci. Rep., 10:277-285) and 80 of the nuclear genes on the 101 gene sequencing panel for mitochondrial disease and related disorders that is currently available in the clinical diagnostic setting at GeneDx (Gaithersburg, Md.). Targeted sequence analysis of the MitoCarta gene set together with the mtDNA genome has been estimated to be likely to identify pathogenic causes in at least 47% of all individuals with suspected primary mitochondrial disease (Calvo et al. (2012) Sci. Transl. Med., 4:118ra110). Therefore, sequence analysis of the MitoCarta nuclear gene set, the mtDNA genome, and the entire nuclear exome can reasonably be expected to facilitate genetic diagnosis in more than half of all patients with suspected mitochondrial disease, while also presenting the simultaneous opportunity for novel disease gene discovery. Such analysis is now technically feasible by application of massively parallel sequencing methodologies that have emerged in both the research and clinical settings.

A single unified platform has not been available to reliably permit simultaneous interrogation of all known and potential causes of suspected mitochondrial disease and phenotypically overlapping disorders. Exome capture kits are not all equally designed, do not capture the same target regions, and do not all perform with the same efficiency. Indeed, the early versions of commercially available whole-exome capture kits were found to target significantly different genomic regions and to vary greatly in their overall performance (Asan et al. (2011) Genome Biol., 12:R95; Kiialainen et al. (2011) PLoS One 6:e16486). In addition, no whole-exome capture kit has been optimized to provide highly reliable capture of the MitoCarta nuclear gene set and to provide targeted capture of the mtDNA genome. While off-target capture of the mtDNA genome is inevitable in any whole-exome capture kit, this is typically highly non-reproducible with insufficient coverage to either provide reliable interrogation of the complete mtDNA genome sequence or sensitively detect heteroplasmic mtDNA mutations.

SUMMARY OF THE INVENTION

In accordance with the present invention, compositions comprising oligonucleotides that specifically hybridize (e.g., are complementary) with mitochondrial DNA are provided. In a particular embodiment, the composition comprises at least one oligonucleotide comprising a nucleic acid molecule set forth in FIG. 6. The composition may comprise at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all of the nucleic acid molecules provided in FIG. 6. The compositions of the instant invention may further comprise oligonucleotides that specifically hybridize with the nuclear genome. In a particular embodiment, the composition further comprises a genome library, exome library, and/or oligonucleotides that specifically hybridize with MitoCarta gene sequences (e.g., those that are not included in the whole exome library, when present). For example, the composition may further comprise oligonucleotides that specifically hybridize with at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all 16 of the following genes: BCL2, GPX1, LYRM4, MSRB2, NDUFA11, NUDT8, PIGY, PRDX2, PRDX5, SLC25A26, TIMM117B, ZBED5, C6orf136, HSD17B8, MRPS18B, and TAP1. In a particular embodiment, the ratio of mitochondrial oligonucleotides to nuclear oligonucleotides is about 1:100. Kits comprising one or more compositions of the instant invention are also provided.

In accordance with another aspect of the instant invention, methods of diagnosing a mitochondrial disease in a subject are provided. The instant invention also encompasses methods for identifying mutations associated with a mitochondrial disease or disorder.

BRIEF DESCRIPTIONS OF THE DRAWING

FIGS. 1A and 1B show that standard 50 Mb whole-exome capture kit has inadequate coverage of 12 nuclear genes in the 1,034 MitoCarta gene set. FIG. 1A shows the median fold-coverage in 8 unrelated human blood DNA samples for all standard 50 Mb target regions and the 12 MitoCarta gene regions that were identified to have suboptimal coverage on the standard 50 Mb whole-exome design. Each sample was sequenced in a single flow-cell lane on the Illumina HiSeq 2000. FIG. 1B provides a graph of the fraction (percent) coverage for all 50 Mb target regions and 12 MitoCarta gene regions at varying depths of coverage from 1× to 20×.

FIGS. 2A and 2B show the coverage analysis of variable mtDNA genome to nuclear capture molar ratios. FIG. 2A provides the median sequence coverage for both the nuclear exome and mtDNA genome for 9 samples captured with different mixes of custom library baits. The first seven sets of bars each represent capture ratios of targeted mtDNA genome (Design C) to nuclear baits (Designs A+B), with molar ratios as labeled. The eighth set of bars indicates a 1:1 ratio of standard 50 Mb whole exome to custom MitoCarta baits for the 12 genes not adequately targeted on the initial design (Designs A+B), but no mtDNA baits were included. The ninth set of bars indicates performance of the standard 50 Mb whole exome platform (Design A). FIG. 2B provides the fraction (percent) of the mitochondrial genome sequenced at variable depths of coverage ranging from 1× to 1000× for the same 9 samples captured with the different molar ratios of custom library baits as described above for FIG. 2A.

FIGS. 3A and 3B show the coverage statistics of 1:100 Mito-Plus Whole Exome capture and Illumina HiSeq NGS analysis of 11 human blood samples. FIG. 3A provides the median coverage for 5 different gene groups from left to right: all 1,034 MitoCarta genes, 12 MitoCarta genes not covered adequately by the standard 50 Mb whole exome kit, 101 nuclear genes on the commercially-available GeneDx Mitochondrial Disease panel, all target regions, and the mtDNA genome. FIG. 3B provides the fraction (percent) coverage mean and standard deviation across all 11 samples for these same 5 gene groupings at 1×, 10×, and 20× depth of coverage. Each sample was run in a single HiSeq flow-cell lane for NGS analysis.

FIG. 4 provides an analysis of maximal influence of nuclear-encoded mitochondrial transcripts (Numts or pseudogenes) on reliable heteroplasmy detection sensitivity. The boxplot conveys the ratio of reads aligned to the mitochondrial DNA genome that might originate from Numt contamination across 9 samples captured with the 1:100 mtDNA:nuclear Mito-Plus Whole-Exome custom capture kit and sequenced one sample per flow-cell lane on the Illumina HiSeq 2000. The length of the box represents the 25th to 75th interquartile range, the interior horizontal line represents the median, and vertical lines issuing from the box extend to the minimum and maximum values of the analysis variable.

FIGS. 5A and 5B show that Mito-Plus Whole Exome capture reliably detects heteroplasmic mtDNA mutations. Coverage distribution statistics for replicate experiments for all targeted regions (FIG. 5A) and the whole mtDNA genome (FIG. 5B) are provided. MF-1 and MF-2 represent separate datasets from two flow-cell lanes run on blood DNA captured with the 1:500 and 1:1000 molar ratios of mtDNA:nDNA, respectively, from the same mitochondrial disease patient having a known mtDNA-encoded ND5 gene heteroplasmic mutation (m.13513G>A).

FIGS. 6A-6L provide the probe sequences targeting the entire mtDNA genome. Sequences provided are SEQ NOs: 1-131, from top to bottom.

FIG. 7 provides the coverage statistics for the entire whole-exome nuclear target regions for 9 samples captured with different mixes of custom library baits.

FIG. 8 shows the coverage performance for both the nuclear exome and mtDNA genome with varying molar ratios of custom baits for the mtDNA genome relative to the MitoCarta-optimized standard 50 Mb whole exome design. Nuclear exome coverage was preserved regardless of mtDNA:nDNA genome capture ratio, but the mtDNA genome median and high-depth (>1,000×) coverage began to fall off at molar ratios below 1:100. Data shown included all sequence reads. Following removal of duplicate sequencing reads, the mtDNA genome coverage fall-off was even more evident beginning at 1:200 molar ratio, where 1,000× coverage was only achieved for 93.29% of the mtDNA genome.

FIG. 9 provides a graph of the estimated sequencing error rate for HiSeq and SOLID platforms based on concurrent analysis of the PhiX genome. Sequencing error rate is shown for each of the individual flow cell lanes on the Illumina HiSeq, as well as for the cumulative SOLiD dataset.

FIGS. 10A-10E provide the Mito 101 gene list and associated disorders. FIG. 10F provides the references cited in FIGS. 10A-10E.

DETAILED DESCRIPTION OF THE INVENTION

Discovering causative genetic variants in individual cases of suspected mitochondrial disease requires interrogation of both the mitochondrial (mtDNA) and nuclear genomes. Whole-exome sequencing can support simultaneous dual-genome analysis, although currently available capture kits do not target the mtDNA genome and provide insufficient capture for some nuclear-encoded mitochondrial genes. To optimize interrogation of nuclear and mtDNA genes relevant to mitochondrial biology and disease, a custom whole-exome library was formulated by blending RNA “baits” from three separate designs: (A) Agilent Technologies SureSelect^(XT) 50 Mb All Exon PLUS Targeted Enrichment Kit, (B) 16-gene nuclear panel targeting sequences for known MitoCarta proteins not included in the 50 Mb All Exon design, and (C) sequences targeting the entire mtDNA genome. The final custom formulations consisted of a 1:1 ratio of nuclear baits to which a 1 to 1,000-fold diluted ratio of mtDNA genome baits were blended. Patient sample capture libraries were paired-end sequenced on an Illumina HiSeq 2000 system using v3.0 SBS chemistry, mtDNA genome coverage varied depending on the mtDNA:nuclear blend ratio, where a 1:100 ratio provided optimal dual-genome coverage with 10× coverage for over 97.5% of all targeted nuclear regions and 1,000× coverage for 99.8% of the mtDNA genome. mtDNA mutations were reliably detected to at least an 8% heteroplasmy level, as discriminated both from sequencing errors and potential contamination from nuclear mtDNA transcripts (Numts). The “1:100 Mito-Plus Whole-Exome” Agilent capture kit offers an optimized tool for whole-exome analysis of nuclear and mtDNA genes relevant to the diagnostic evaluation of mitochondrial disease. This platform provides a one-stop whole-exome sequencing solution that can be applied to both research and clinical genetic diagnostic evaluations of individuals with suspected mitochondrial disease.

While mitochondrial diseases are relatively rare and many are poorly understood, the causes of certain mitochondrial diseases have been identified (see, e.g., FIG. 10). The cause of the mitochondrial diseases may be mutations in mitochondrial DNA or nuclear DNA. The instant invention provides an optimized tool for whole exome analysis of nuclear and mtDNA genes relevant to the diagnostic evaluation of mitochondrial disease. The library of the instant invention allows for simultaneous enrichment for subsequent next-generation sequencing based sequence analysis of MitoCarta nuclear genes and the entire mtDNA genome, as is highly relevant to the diagnostic evaluation of suspected mitochondrial disease. By being embedded in a whole-exome capture kit, this mitochondrial-optimized genomic analysis nevertheless retains the simultaneous opportunity for discovery both of phenotypically-overlapping disorders that may not directly involve the mitochondria as well as of novel disease genes. The data presented herein indicates that the custom “1:100 Mito-Plus Whole-Exome” design offers reliable mtDNA mutation heteroplasmy detection sensitivity together with the distinct advantage that no separate technical or analytic methodologies for mtDNA genome sequence analysis are required by the investigator at the time of sample processing for whole-exome analysis. This design allows for targeted enrichment of the whole-exome for sequence-based genetic diagnosis in both research and clinical diagnostic applications where the relevance of mtDNA is well-recognized, as well as in cases where the potential contributory role of mtDNA mutations may otherwise be overlooked.

In accordance with the instant invention, compositions comprising oligonucleotides which specifically hybridize with mitochondrial DNA are provided. The oligonucleotides may be RNA or DNA, particularly DNA. The oligonucleotides may be single-stranded or double-stranded. The oligonucleotides may also vary in length. For example, oligonucleotides of the instant invention may be about 10 to about 500 nucleotides in length, about 20 to about 250 nucleotides in length, or about 50 to about 200 nucleotides in length. The compositions may optionally comprise at least one carrier (e.g., a liquid buffer or aqueous solution). Alternatively, the oligonucleotides may be dried or lyophilized for re-suspension later. In a particular embodiment, the oligonucleotides of the instant invention are contained within a microarray or immobilized on a solid support.

In a particular embodiment, the composition comprises at least one oligonucleotide comprising a nucleic acid molecule in FIG. 6 (or oligonucleotides complementary to those in FIG. 6). The composition may comprise at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all of the nucleic acid molecules provided in FIG. 6. The oligonucleotides may comprise the sequences provided in FIG. 6, consist of the sequences provided in FIG. 6, or be a fragment of the sequences provided in FIG. 6 (e.g., a fragment of about 100 nucleotides in length). In a particular embodiment, the compositions of the instant invention comprise oligonucleotides with at least one variant of the sequences provided in FIG. 6. The variant may have at least 90%, 95%, 97%, or 99% homology (identity) with the sequence provided in FIG. 6.

The compositions of the instant invention may further comprise oligonucleotides that specifically hybridize with the nuclear genome. In a particular embodiment, the composition further comprises a genome library or a whole exome library (e.g., oligonucleotides that specifically hybridize with exons) such as the SureSelect 50 Mb Human All-Exon library. In a particular embodiment, the composition may further comprise oligonucleotides that specifically hybridize with MitoCarta gene sequences that are not included in the whole exome library. For example, the composition may further comprise oligonucleotides which specifically hybridize with at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all 16 of the following genes (inclusive of coding regions and UTRs): BCL2, GPX1, LYRM4, MSRB2, NDUFA11, NUDT8, PIGY, PRDX2, PRDX1, SLC25A26, TIMMI17B, ZBED5, C6orf136, HSD17B8, MRPS18B, and TAP1.

When the compositions of the instant invention comprise oligonucleotides that specifically hybridize with the nuclear genome or exome and oligonucleotides that specifically hybridize with mitochondrial DNA, the ratio of mitochondrial oligonucleotides to nuclear oligonucleotides can be varied. In a particular embodiment, the ratio of mitochondrial oligonucleotides to nuclear oligonucleotides ranges from about 10:1 to about 1:1000, about 1:1 to about 1:500, about 1:10 to about 1:250, about 1:50 to about 1:200, about 1:75 to about 1:150, about 1:90 to about 1:110, or about 1:100.

The oligonucleotides of the instant invention may also be contained in a kit. Within the kit, the mitochondrial oligonucleotides may be contained in a first composition and the nuclear oligonucleotides may be contained in a second composition. Alternatively, the kit may comprise a single composition comprising the mitochondrial oligonucleotides and, optionally, the nuclear oligonucleotides. The kit may further comprise instruction material, buffers, and/or containers.

The instant invention also provides methods of diagnosing and/or determining the susceptibility to/risk and/or providing a prognosis for a mitochondrial disease in a subject (e.g., mammal, human). FIG. 10 provides examples of various mitochondrial diseases/disorders and the causative genetic mutation. The methods of the invention may comprise sequencing the nucleic acid molecules in a biological sample obtained from the subject by obtaining or isolating nucleic acid molecules from the biological sample with the oligonucleotides of the instant invention, amplifying the nucleic acid molecules, and determining the presence or absence of mutation associated with a mitochondrial disease in the amplified. DNA. The methods of the invention may comprise sequencing the nucleic acid molecules in a biological sample obtained from the subject by performing PCR with the oligonucleotides of the instant invention and determining the presence or absence of mutation associated with a mitochondrial disease in the amplified DNA.

In addition to the above, the instant invention also encompasses methods for identifying mutations associated with a mitochondrial disease or disorder. In a particular embodiment, the method comprises sequencing the nucleic acid molecules of a biological sample as described above, wherein a mutation in a nucleic acid molecule compared to wild-type is indicative of a mutation associated with a mitochondrial disease or disorder. In a particular embodiment, a population of biological sample from more than one subject with the mitochondrial disease or disorder is assayed in the method.

DEFINITIONS

The following definitions are provided to facilitate an understanding of the present invention:

The singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.

As used herein, a “biological sample” refers to a sample of biological material obtained from a subject, preferably a human subject, including a tissue, a tissue sample, a cell sample, a tumor sample, and a biological fluid (e.g., blood, urine, or amniotic fluid). In a particular embodiment, the biological sample is blood.

As used herein, “diagnose” refers to detecting and identifying a disease or disorder in a subject. The term may also encompass assessing or evaluating the disease or disorder status (progression, regression, stabilization, response to treatment, etc.) in a patient known to have the disease or disorder.

As used herein, the term “prognosis” refers to providing information regarding the impact of the presence of a disease or disorder (e.g., as determined by the diagnostic methods of the present invention) on a subject's future health (e.g., expected morbidity or mortality, the likelihood of getting diabetes, and the risk of cardiovascular disease). In other words, the term “prognosis” refers to providing a prediction of the probable course and outcome of a disease/disorder or the likelihood of recovery from the disease/disorder.

The term “treat” as used herein refers to any type of treatment that imparts a benefit to a patient afflicted with a disease or disorder, including improvement in the condition of the patient (e.g., in one or more symptoms), delay in the progression of the condition, etc.

The term “probe” as used herein refers to an oligonucleotide, polynucleotide or nucleic acid, either RNA or DNA, whether occurring naturally as in a purified restriction enzyme digest or produced synthetically, which is capable of annealing with or specifically hybridizing to a nucleic acid with sequences complementary to the probe. A probe may be either single-stranded or double-stranded. The exact length of the probe will depend upon many factors, including temperature, source of probe and use of the method. For example, for diagnostic applications, depending on the complexity of the target sequence, the oligonucleotide probe typically contains about 10-500, about 10-250, about 10-100, about 10-50, about 15-30, about 15-25, about 20-50, or more nucleotides, although it may contain fewer nucleotides. The probes herein may be selected to be complementary to different strands of a particular target nucleic acid sequence. This means that the probes must be sufficiently complementary so as to be able to “specifically hybridize” or anneal with their respective target strands under a set of pre-determined conditions. Therefore, the probe sequence need not reflect the exact complementary sequence of the target, although they may. For example, a non-complementary nucleotide fragment may be attached to the 5′ or 3′ end of the probe, with the remainder of the probe sequence being complementary to the target strand. Alternatively, non-complementary bases or longer sequences can be interspersed into the probe, provided that the probe sequence has sufficient complementarity with the sequence of the target nucleic acid to anneal therewith specifically.

The term “primer” as used herein refers to an oligonucleotide, either RN⁻A or DNA, either single-stranded or double-stranded, either derived from a biological system, generated by restriction enzyme digestion, or produced synthetically which, when placed in the proper environment, is able to functionally act as an initiator of template-dependent nucleic acid synthesis. When presented with an appropriate nucleic acid template, suitable nucleoside triphosphate precursors of nucleic acids, a polymerase enzyme, suitable cofactors and conditions such as appropriate temperature and pH, the primer may be extended at its 3′ terminus by the addition of nucleotides by the action of a polymerase or similar activity to yield a primer extension product. The primer may vary in length depending on the particular conditions and requirement of the application. For example, in diagnostic applications, the oligonucleotide primer is typically about 10-25 or more nucleotides in length, but can be significantly longer. The primer must be of sufficient complementarity to the desired template to prime the synthesis of the desired extension product, that is, to be able to anneal with the desired template strand in a manner sufficient to provide the 3′ hydroxyl moiety of the primer in appropriate juxtaposition for use in the initiation of synthesis by a polymerase or similar enzyme. It is not required that the primer sequence represent an exact complement of the desired template. For example, a non-complementary nucleotide sequence may be attached to the 5′ end of an otherwise complementary primer. Alternatively, non-complementary bases may be interspersed within the oligonucleotide primer sequence, provided that the primer sequence has sufficient complementarity with the sequence of the desired template strand to functionally provide a template-primer complex for the synthesis of the extension product.

Polymerase chain reaction (PCR) has been described in U.S. Pat. Nos. 4,683,195, 4,800,195, and 4,965,188, the entire disclosures of which are incorporated by reference herein.

With respect to single stranded nucleic acids, particularly oligonucleotides, the term “specifically hybridizing” refers to the association between two single-stranded nucleotide molecules of sufficiently complementary sequence to permit such hybridization under pre-determined conditions generally used in the art (sometimes termed “substantially complementary”). in particular, the term refers to hybridization of an oligonucleotide with a substantially complementary sequence contained within a single-stranded DNA molecule of the invention, to the substantial exclusion of hybridization of the oligonucleotide with single-stranded nucleic acids of non-complementary sequence. Appropriate conditions enabling specific hybridization of single stranded nucleic acid molecules of varying complementarity are well known in the art.

For instance, one common formula for calculating the stringency conditions required to achieve hybridization between nucleic acid molecules of a specified sequence homology is set forth below (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press):

Tm=81.5° C.+16.6 Log [Na+]+0.41(% G+C)−0.63 (% formamide)−600/# bp in duplex

As an illustration of the above formula, using [Na+]=[0.368] and 50% formamide, with GC content of 42% and an average probe size of 200 bases, the Tm is 57° C. The Tm of a DNA duplex decreases by 1-1.5° C. with every 1% decrease in homology, Thus, targets with greater than about 75% sequence identity would be observed using a hybridization temperature of 42° C.

The stringency of the hybridization and wash depend primarily on the salt concentration and temperature of the solutions. In general, to maximize the rate of annealing of the probe with its target, the hybridization is usually carried out at salt and temperature conditions that are 20-25° C. below the calculated Tm of the hybrid. Wash conditions should be as stringent as possible for the degree of identity of the probe for the target. In general, wash conditions are selected to be approximately 12 20° C. below the Tm of the hybrid. In regards to the nucleic acids of the current invention, a moderate stringency hybridization is defined as hybridization in 6×SSC, 5× Denhardt's solution. 0.5% SDS and 100 μg/ml denatured salmon sperm DNA at 42° C., and washed in 2×SSC and 0.5% SDS at 55° C. for 15 minutes. A high stringency hybridization is defined as hybridization in 6×SSC, 5× Denhardt's solution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNA at 42° C., and washed in 1×SSC and 0.5% SDS at 65° C. for 15 minutes, A very high stringency hybridization is defined as hybridization in 6×SSC, 5× Denhardt's solution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNA at 42° C., and washed in 0.1×SSC and 0.5% SDS at 65° C. for 15 minutes.

The term “isolated” may refer to a compound or complex that has been sufficiently separated from other compounds with which it would naturally be associated. “Isolated” is not meant to exclude artificial or synthetic mixtures with other compounds or materials, or the presence of impurities that do not interfere with fundamental activity or ensuing assays, and that may be present_(;) for example, due to incomplete purification, or the addition of stabilizers,

As used herein, an “instructional material” includes a publication, a recording, a diagram, or any other medium of expression which can be used to communicate the usefulness of the composition of the invention for performing a method of the invention.

The phrase “solid support” refers to any solid surface including, without limitation, any chip (for example, silica-based, glass, or gold chip), glass slide, membrane, plate, bead, solid particle (for example, agarose, sepharose, polystyrene or magnetic bead), column (or column material), test tube, or microtiter dish.

As used herein, the term “array” refers to an ordered arrangement of hybridizable array elements (e.g., proteins, nucleic acids, antibodies, etc.). The array elements are arranged so that there are at least one or more different array elements on a solid support. In a particular embodiment, the array elements comprise oligonucleotide probes. In a particular embodiment, the arrays comprise up to about 50, up to about 100, up to about 500, up to 1000, up to about 5,000, up to 10,000, up to 50,000, up to 100,000 or more nucleic acid molecules/probes (e.g., to unique nucleic acid targets).

“Pharmaceutically acceptable” indicates approval by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.

A “carrier” refers to, for example, a diluent, adjuvant, excipient, auxiliary agent or vehicle with which an active agent of the present invention is administered. Carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Other examples of liquid carriers include aqueous saline solutions and aqueous dextrose and glycerol solutions. Suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin (e.g., Remington's Pharmaceutical Sciences (Mack Publishing Co., Easton, Pa.)) and “Remington: The Science and Practice of Pharmacy” (Ed. Troy; Lippincott Williams & Wilkins, Baltimore, Md.).

The following example provides illustrative methods of practicing the instant invention, and is not intended to limit the scope of the invention in any way.

EXAMPLE Materials and Methods

mtDNA Genome Bail and Blend Design.

Sequences targeting the entire mtDNA genome were created in eArray (Agilent Technologies) by standard 1× tiling across the target hg19 mitochondrial loci. These baits for “Design C” (mtDNA genome) were factory-blended into the nuclear baits at either equimolar ratio or reduced concentration by 10, 50, 100, 200, 500, or 1000-fold less than the nuclear baits. The accession number for the Agilent mtDNA genome design bait library was ELID #320851

(earray.chem.agilent.com/earray).

Nuclear Mitochondrial Gene Set Optimization.

Bioinformatics analysis of the SureSelect^(XT) 50 Mb All Exon PLUS Targeted Enrichment Kit was performed to determine the exon level coverage of 1,034 known mitochondria-localized “Human MitoCarta” genes (Pagliarini et al. (2008) Cell 134:112-123). Baits were designed for 16 of these nuclear genes shown to have less than 80% of their exons covered (ELID #329521) (earray.chem.agilent.com/earray). These baits were factory-added in equimolar ratio to the SureSelectXT 50 Mb All Exon PLUS Targeted Enrichment (Agilent part number 5190-2867).

Exome Sequencing.

Targeted enrichment was performed using Agilent Technologies SureSelect^(XT) 50 Mb All Exon PLUS Targeted Enrichment Kit that included custom mitochondrial genome content in varying mitochondrial: nuclear capture bait molar ratios, namely: Blend A—1:1; Blend B—1:10; Blend C—1:50; Blend D—1:100; Blend E—1:200; Blend F—1:500; Blend G—1:1000. Patient sample capture libraries were prepared as described in the kit manual, and were 2×101 base pair paired-end sequenced on an Illumina (San Diego, Calif.) HiSeq 2000 Next-Generation Sequencing system using v3.0 SBS chemistry with average flow-cell lane cluster densities of ˜700-800 K/mm². One sample was analyzed per flow-cell lane to obtain a minimum 10× read depth of ˜96% for the targeted nuclear exome. The mitochondrial genome coverage varied depending on the mitochondrial: nuclear blend ratio.

Exome Data Analyses.

Burrows-Wheeler Aligner (BW A) (version 0.5.9-r16) was used to align the sequence reads to the human reference genome GRCh37 downloaded from the 1000 Genomes Project website (www.1000genomes.org/). Samtools (version 0.1.12 or r859) was used to remove potential duplicates (with rmdup command), and make initial single nucleotide polymorphism (SNP) and indel calls (with pileup command). A custom program was developed and used to further refine the SNP and indel calls. The custom program uses a false discovery rate approach to adjust raw base counts at a candidate position after Benjamini and Hochberg correction based on quality values of all bases. A coverage depth cutoff of 10× is then applied. Depth of coverage is calculated based on the alignment file using samtools.

Sequencing Error Estimation Using PhiX Phage Genome.

BWA (version 0.5.9-r16) was used to align HiSeq sequence reads to the PhiX phage genome (NC_001422.1) downloaded from NCBI. BioScope was used at default settings to align SOLID sequence data. Samtools was applied to remove duplicates and obtain the number of high quality base reads for different strands and alternative bases at a given base position. Sequencing error rate was estimated as the sum of the number of bases different from the consensus call made by Samtools over the depth of coverage at a given base position.

Results

Agilent SureSelect 50 Mb Standard Whole-Exome Capture Kit Provides Insufficient Coverage for the mtDNA Genome and all MitoCarta Genes.

The target regions of the Agilent SureSelect 50 Mb whole-exome capture kit (“50 Mb kit”) do not include the mtDNA genome, as no probes specifically capture mtDNA. Although off-target capture from this platform does provide some mtDNA genome coverage, this is of questionable specificity and is insufficient to permit reliable sequence analysis across the entirety of the mtDNA genome. An in silico comparison of 50 Mb kit target regions with the reference sequence gene set (NCBI RefSeq) revealed that among the 1,034 MitoCarta genes there were 12 nuclear genes (BCL2, GPX1, LYRM4, MSRB2, NUDFA11, NUDT8, PIGY, PRDX2, PRDX5, SLC25A26, TIMM117B, ZBED5) that had less than 80% of their exonic regions covered by the target regions of the 50 Mb kit. Lack of coverage for these genes was empirically confirmed by analysis of 8 exomes captured with the standard 50 Mb kit that were sequenced in a single sample per flow-cell lane on the Illumina HiSeq 2000 (FIG. 1A). The average whole-exome coverage for each sample ranged from 159.7× to 351.8×, with 98.0% to 99.1% of all target regions covered at least 1×. By comparison, the 12 MitoCarta genes in question had not only a lower average depth of coverage (range: 69.8×-170.9×) but also a markedly lower percentage of exonic regions that were covered at least 1× (range: 78.4% to 84.9%) (FIG. 1B). Experimental evidence demonstrated that lack of sequence coverage for these 12 MitoCarta nuclear genes was even more pronounced at the standard 10× and 20× depth-of-coverage cutoffs that are typically used for variant calling purposes.

SureSelect Custom Probe Design to Optimize Coverage of the mtDNA Genome and All MitoCarta Genes.

A custom SureSelect “Mito-Plus Whole-Exome” library was generated by blending RNA “baits” from 3 separate designs: (A) standard SureSelect 50 Mb Human All-Exon product that targets the nuclear exome, (B) a 16-gene panel targeting MitoCarta gene sequences that were not included in the All-Exon design, and (C) sequences targeting the entire mtDNA genome (FIG. 6). Designs B and C were created in eArray by 2× tiling across target nuclear genes or 1× tiling across the target hg19 mtDNA genome loci, respectively. Baits having significant overlap with RepeatMasker regions were excluded. For Design B, new nuclear genome baits targeted 416 additional coding regions and 186 UTRs in total for the 12 MitoCarta genes that were suboptimally targeted by the 50 Mb kit (BCL2, GPX1, LYRM4, MSRB2, NDUFA11, NUDT8, PIGY, PRDX2, PRDX5, SLC25A26, ZBED5), as well as exonic regions of 4 other MitoCarta nuclear genes present on alternative genome assemblies (C6orf136, HSD17B8, MRPS18B, TAP1) (bait details available upon request). The 3 different designs were factory blended in varying molar ratios of Designs A plus B to Design C, as detailed below, for purposes of optimizing dual genome capture of mitochondrial genes.

Experimental Evaluation of the Optimal Capture Ratio of mtDNA to Nuclear Baits.

All final custom formulations consisted of a 1:1 ratio of nuclear baits from Design A (All-Exon) to Design B (16 MitoCarta genes). Given the 1-2 log natural excess of mtDNA genomes to the nuclear genome, the optimal output of nuclear versus mtDNA genome sequences that retained the ability to detect low-level mtDNA variant heteroplasmy was sought. Therefore, a range of seven molar concentrations of all nuclear baits (Designs A plus B) to Design C (mtDNA genome) baits was experimentally evaluated. Design C (mtDNA genome) baits were blended in at either an equimolar ratio or reduced concentrations of 10, 50, 100, 200, 500, or 1000-fold less than the nuclear baits. Subsequently, 9 randomly selected human blood DNA samples were selected for capturing each by one of these 7 different molar ratios (labeled from A to G to indicate 1:1, 1:10, 1:50, 1:100, 1:200, 1:500, and 1:1000), a 1:1 ratio of Design A to Design B (with no mtDNA genome baits added), or the standard 50 Mb kit (FIG. 7). The 9 captured DNA samples were then sequenced in a single flow-cell lane for each sample on the Illumina HiSeq 2000. Optimal coverage across the entire nuclear exome target regions was achieved for each of the 9 samples regardless of the mtDNA:nDNA molar ratio (FIG. 2A and FIG. 7). Specifically, 99.0% to 99.4% of whole-exome nuclear target regions were covered at least 1×, with 96.0% to 98.1% of whole-exome nuclear target regions covered at least 10× (FIG. 8). Even at an equimolar ratio of 1:1 mtDNA:nuclear exome capture, the overall performance statistics for nuclear exome sequence coverage did not differ either in median coverage or in percentage of target regions covered at 1×, 10×, or 20× relative to either the standard 50 Mb kit alone or combined with the Design B (MitoCarta gene) nuclear probes.

Similarly, the standard 50 Mb kit that contained no mtDNA baits still provided some mtDNA genome coverage, which was 100% at 1× coverage and 99.99% at 10× coverage (FIG. 2B). This off-target mtDNA capture is explained by the greater natural abundance in terms of molar ratio of mtDNA to nuclear DNA. Nonetheless, such non-targeted coverage is obviously random, non-uniform, drops significantly upon analysis of 100× coverage performance, and has a minimum coverage depth of 0 to 2 reads at some mtDNA genome bases. Whereas 10× to 20× median coverage is generally acceptable for analysis of nuclear exome capture performance, a substantially higher-depth of coverage across the entire mtDNA genome is critical to permit reliable detection of low-level mtDNA variant heteroplasmy. Mixing mtDNA genome baits with nuclear baits at all 7 different ratios, from equimolar to 1 mtDNA to 1000 nDNA, all provided much improved coverage across the entire mtDNA genome. Specifically, the standard 50 Mb kit had a median 109× and mean of 133.5× mtDNA genome coverage. However, careful data analysis suggested that the optimal mtDNA:nuclear molar ratio was 1:100, where over 99.9% of the mtDNA genome was covered at least 100×, over 99.8% of the mtDNA genome was covered at least 1000×, the median coverage was 7,918×, and the minimum depth of coverage for any mtDNA base was 41×. Higher molar ratios (1:1, 1:10, 1:50) provided similar if not better mtDNA coverage as seen with 1:100, but these higher molar ratios carry the potential cost of reducing sequencing bandwidth in the nuclear target regions. Lower molar ratios (1:200, 1:500, 1:1000) demonstrated a progressive fall-off in mtDNA genome coverage, which for the 1:200 ratio was an mtDNA genome median coverage of 4,497× with only 99.1% of the mtDNA genome covered to a depth of 1000×. Therefore, a 1:100 mtDNA to nuclear molar ratio was selected for subsequent experiments.

A 1:100 Molar Ratio of mtDNA to Nuclear Baits Provided Optimal Coverage for Both the Nuclear Target Regions and the mtDNA Genome.

Custom libraries with 1:100 molar ratio of mtDNA to nuclear baits were used to capture 11 exomes from human blood genomic DNA and then sequenced using one HiSeq 2000 flow-cell lane per sample, with coverage statistics summarized in FIG. 3A. Although capture experiments did not work as well for two samples (61p2 and 79) as they did for the other 9 samples, 1× coverage of the nuclear exome was seen for 98.4% to 99.7% of target regions for each of the 11 samples tested. Excluding the two samples that had suboptimal performance, an average of 194× to 415× mean depth of coverage for the nuclear exome was achieved for the remaining 9 samples. Optimal mtDNA genome coverage was achieved for all 11 samples (FIG. 3B), which was 99.99% to 100% of mtDNA genome bases covered at both 1× and 10×, 99.89% to 100% of mtDNA genome bases covered at 100× coverage, and 93.75% to 99.95% of mtDNA genome bases covered at 1000× for all samples. When excluding the two samples that had had suboptimal overall nuclear and mtDNA capture performance (61p2 and 79), 1000× coverage was seen at 99.6% to 99.95% of all mtDNA genome bases in each of the remaining 9 samples captured at the 1:100 mtDNA to nuclear molar ratio.

All MitoCarta Nuclear Genes are Well-Covered by the SureSelect Custom 1:100 “Mita-Plus Whole-Exome” Capture Kit.

Given the relevance of the MitoCarta nuclear gene list to candidate gene analysis in the diagnostic evaluation of suspected mitochondrial disease, it was examined how well the exonic regions of 1,034 MitoCarta genes were covered on the custom 1:100 “Mito-Plus Whole Exome” capture kit. In this analysis, all exonic regions of these 1,034 MitoCarta genes were looked at, rather than just the targeted exonic regions for which new baits had been designed. At least 97.9% of exonic regions for all Mitocarta genes were covered at least 1× when including the two samples (61p2 and 79) that had generally suboptimal coverage (FIG. 3B), while more than 99.1% of exonic regions for all MitoCarta genes had 1× coverage in each of the 9 samples that had good overall performance. Improved coverage was also evident for the 12 MitoCarta genes whose exons were not sufficiently covered by 50 Mb kit design (not including the 4 genes for which baits were added for exons present on alternative assemblies), with 96.8% to 100% of all exonic regions of these genes covered at least 1× in all 11 samples (FIG. 3B). Excluding the two relatively poor-performing samples (61p2 and 79), 10× coverage was achieved for 96.8% to 98.1%, and at least 20× coverage was achieved for 95.6% to 97.5%, of the exonic regions of these 12 MitoCarta genes. Thus, these data demonstrate the improved utility of this custom capture kit for whole-exome nuclear gene sequence analysis that includes all known mitochondrial-localized proteins (MitoCarta subset) in suspected mitochondrial disease.

Since an important potential use of this custom capture platform would be in the clinical diagnostic setting to provide focused sequencing of all known mitochondrial disease genes (rather than all mitochondrial-localized proteins), the performance of the custom kit to cover 101 known mitochondrial disease genes that are currently sequenced on a clinical diagnostic basis was assessed using next generation sequencing (NGS) by a Mito 101 Mitochondrial Disease Nuclear Gene Panel (GeneDx). All 11 samples had at least 1× coverage across 98.17% to 99.93% of these 101 genes. Upon exclusion of the two problematic samples (61p2 and 79), 10× coverage was achieved for 97.44% to 98.76%, and at least 20× coverage for 94.35% to 98.02%, in each of the remaining 9 samples for these 101 known mitochondrial disease genes. Future work could focus on assessing patterns of specific nucleotide bases that might be systematically missed by current probes that are captured by design of additional probes to achieve improved capture of all possible bases in currently known, and newly recognized, mitochondrial disease genes, In addition, the same custom Design B (MitoCarta genes) and Design C (mtDNA genome) probes that were designed can be added with no alteration in expected coverage performance to the recently released v4.0 Agilent whole-exome kit, which targets the same genomic regions as the standard 50 Mb All-Exon design but is rebalanced to provide more even coverage across the 50 Mb nuclear exome (www.genomics.agilent.com).

mtDNA Genome Heteroplasmy Detection.

Sensitive detection of low-level heteroplasmic mtDNA mutations is critical to the diagnostic evaluation of suspected mitochondrial disease. While the historic “gold-standard” methodology of mtDNA genome analysis by PCR amplification and Sanger sequencing has a lower detection limit ranging between 30-50% heteroplasmy, it is widely recognized that disease may result from lower heteroplasmy levels for some pathogenic mutations that might only be detectable with alternative molecular biology methods such as ARMS (allele refractory mutation system) qPCR (Wang et al. (2011) Curr, Protoc. Hum. Genet., Chapter 19:Unit 19.16). Further, since heteroplasmy levels can vary between tissues in a given patient, it is desirable to achieve sensitive and reproducible detection of potential heteroplasmic mutations that are at low level in blood to avoid pursuit of invasive tissue biopsies to obtain skeletal muscle or liver in which the mutation level might be enriched, For these reasons, NGS has emerged as the preferred molecular method for mtDNA genome analysis in the clinical diagnostic setting. However, NGS-based mtDNA genome analysis is not currently available in a single platform together with whole-exome nuclear gene analysis, but must be separately considered as a potential etiology in a given patient.

To permit low-level heteroplasmy detection, it is necessary to achieve a very high depth of coverage for the mtDNA genome. However, it is important to recognize that the lower bound of sensitivity for heteroplasmy detection is inherently dependent on several platform-specific parameters including sequencing quality and error rate, For example, with an average base quality (Q) score of 30, heteroplasmy as low as 0.1% can be detected when the base is covered to a depth of coverage over 1000×. When the average base Q score is reduced to 20, heteroplasmy levels as low as 1% can still theoretically be detected, although the true heteroplasmy sensitivity is limited by various sequencing platform-specific errors and alignment errors. It is also compounded by the multiple testing problem facing all genomic sequencing applications, including whole exome sequencing. As an example, exome sequencing might reveal reads with variant bases aligned at hundreds of thousands genomic positions, even though the number of coding variants per individual is expected to be around 20,000. It was, therefore, sought to experimentally determine the true heteroplasmy sensitivity of the Mita-Plus whole exome capture design.

Sequencing platform-specific error rates directly influence the likelihood that a given mtDNA variant detected in only a small fraction of the NGS reads represents true heteroplasmy versus a sequencing-related error. The PhiX phage genorne provides a robust means by which to estimate alignment errors due to its genome's simplicity and no concern for potential heteroplasmic sites. Analysis of the PhiX genome that were spiked into the Illumina HiSeq 2000 runs of Agilent Mito-Plus Whole Exome captured nuclear and mtDNA revealed a sequencing error rate of 5.79%+0.42%. This sequencing error is similar to the approximately 5% error rate previously observed when analyzing the PhiX genome that was simultaneously sequenced on the SOLiD 3.0 NGS sequencing platform of the mtDNA genome (see FIG. 1), where the mtDNA genome was amplified by the same two long-range PCR reactions as are used for Affymetrix MitoChip v2.0 analysis (Maitra et al. (2004) Genome Res., 14:812-819; Xie et al. (2011) BMC Bioinformatics 12:402), Thus, Illumina HiSeq 2000 and SOLiD 3.0 technologies have similar rates of sequencing error rates in the 5-6% range, which represents the estimated lower bound of being able to confidently discern truly heteroplasmic mtDNA mutations from machine-generated sequencing error. Thus, low-levels of heteroplasmic mtDNA mutations can be reliably detected following different capture and sequencing technologies, but only to the limit determined by the platform-specific sequencing error rate.

mtDNA heteroplasmy detection sensitivity by NGS is further complicated by the existence of pseudogenes in the nuclear genome that are non-functional but share strong sequence similarity with mtDNA genes (Li et al. (2012) Nucleic Acids Res., 40:e137; Li et al. (2012) Genome Biol., 13:R34). These mtDNA pseudogenes are evolutionary remnants that result from transfer of cytoplasmic mitochondrial DNA sequences into the separate nuclear genome of a eukaryotic organism and are collectively referred to as “nuclear mitochondrial DNA transcripts” (Numt) (Mishmar et al. (2004) Hum. Mutat., 23:125-133), The analytic challenge is that an apparently heteroplasmic mtDNA mutation might instead represent off-target Numt capture that was subsequently aligned to the mtDNA genome because of the strong sequence similarities between mtDNA genes and Numts. To understand the potential influence of Numt on heteroplasmy detection sensitivity, the maximum likelihood that a seemingly heteroplasmic mutation was contaminated by a Numt was estimated. All reads from each sample were first aligned to a reference that includes all known Numts (details available upon request), as well as the mtDNA genome. The number of reads that aligned to the mtDNA genome were counted. All reads were next aligned only to the Numts. The percentage of reads that aligned to the mtDNA genome when the Numts reference was included that can also be aligned to Numts when the mtDNA genome reference is absent provides the upper-bound estimate of the percentage of sequencing reads that align to mtDNA genome but could potentially have originated from Numt contamination. This analysis was performed for 9 randomly selected samples captured by the custom 1:100 mtDNA to nuclear whole-exome capture kit and each sequenced on one HiSeq 2000 flow-cell lane. In all 9 samples, the upper bound of Numt contribution to heteroplasmy sensitivity detection ranged from 7.80% to 8.31% (8.10+0.18%) (FIG. 4). Based on this observation, it can be concluded with greater than 99.9% confidence that an observed heteroplasmic mutation is not from Numt contaminations if it is present in at least 8.64% of sequence reads. However, this is a very conservative estimate since it does not take into account the fact that mtDNA outnumbers nuclear DNA by 1-2 log orders of magnitude (Li et al. (2012) Nucleic Acids Res., 40:e137; Li et al. (2012) Genome Biol., 13:R34). Thus, the true lower bound for mtDNA heteroplasmy detection sensitivity is likely much lower than 8%. Still, even 8% heteroplasmy detection sensitivity already represents great improvement over the 30% to 50% lower bound for mtDNA heteroplasmy detection that is achieved by the “gold-standard” of Sanger sequencing. More importantly, 8% falls below the level of heteroplasmy for a pathogenic mtDNA mutation that is generally likely to cause clinical manifestations of classic mitochondrial disease. While alternative mtDNA capture approaches such as long-range PCR may provide even greater heteroplasmy sensitivity, and even permit large deletion detection by NGS analysis (Zhang et al. (2012) Clin. Chem., 58:1322-1331), these data demonstrate that the Agilent custom “1:100 Mito-Plus Whole-Exome” kit offers good heteroplasmy detection sensitivity together with the distinct advantage that no separate technical or analytic methodologies for mtDNA genome sequence analysis are required at the time of sample processing for whole-exome analysis.

Technical Reproducibility.

The technical reproducibility of the custom “Mito-Plus whole-exome” kit to capture both nuclear exome targets and the mtDNA genome was examined. Two capture libraries were separately prepared using the 1:500 (sample “MF1”) and 1:1000 (sample “MF2”) blend of mtDNA genome to whole-exome design using blood genomic DNA from the same mitochondrial disease patient. Each library was further split into two, differentially bar-coded, and then sequenced in separate HiSeq 2000 flow-cell lanes. Therefore, this data set provides technical replicates both at the library preparation and sequencing levels. Highly reproducible coverage statistics was obtained. Overall short reads alignment characterizations/traits were strongly correlated among technical replicates for all target regions (FIG. 5A) and specifically for the mtDNA genome (FIG. 5B), as correlation coefficients for both analyses were approximately 1.

In addition, this sample was used to assess the technical reproducibility of heteroplasmic mtDNA mutation detection by this platform since the sample was shown by Sanger-based sequencing to harbor a 30% heteroplasmic G to A transition mutation at position 13513 of the mt-ND5 gene. The mt-ND5 heteroplasmic mutation was present at a level of 65.0% (723 A/1112 total reads) in the MF1-1 data set, at a level of 64.9% (803 A/1238 total reads) in the MF1-2 data set, at a level of 63.4% (393 A/620 total reads) in the MF2-1 data set, and at a level of 64.8% (411 A/634 total reads) in the MF2-2 data set. Thus, heteroplasmy level determination from the mtDNA sequence data generated is highly reproducible, and likely more accurate than traditional Sanger sequencing, as is consistent with the growing recognition that NGS is becoming the new “gold-standard” for mtDNA heteroplasmy detection over Sanger sequencing (Zhang et al., 2012).

Biological Discovery.

The 11 exomes from human blood genomic DNA that were sequenced following capture with the custom “1:100 Mito-Plus Whole-Exome” design were from probands and family members in 4 unrelated mitochondrial disease families (FIG. 3A). Ideal coverage was achieved for most of these samples across both nuclear exome and mitochondrial genomes (FIG. 3A). This allows exclusion of mtDNA mutations as the disease cause for each family, while focusing on the identification of mutations in nuclear genes as strong novel disease gene candidates in these mitochondrial disease families.

A custom “1:100 Mito-Plus Whole-Exome” Agilent capture kit has been developed that allows simultaneous enrichment for subsequent NGS-based sequence analysis of all currently known nuclear MitoCarta genes and the entire mtDNA genome, as is highly relevant to the diagnostic evaluation of suspected mitochondrial disease. By being embedded in a whole-exome capture kit, this mitochondrial-optimized analysis nevertheless retains the simultaneous opportunity for discovery both of phenotypically-overlapping disorders that may not directly involve the mitochondria as well as of novel disease genes. Further, the data supports that the custom “1:100 Whole-Exome” design offers reliable mtDNA mutation heteroplasmy detection sensitivity together with the distinct advantage that no separate technical or analytic methodologies for mtDNA genome sequence analysis are required by the investigator at the time of sample processing for whole-exome analysis. Thus, this design holds value for providing targeted enrichment of the whole-exome for sequence-based genetic diagnosis in both research and clinical diagnostic applications where the relevance of mtDNA is well-recognized, as well as in cases where the potential contributory role of mtDNA mutations may otherwise be overlooked. Future utilization of this capture approach in larger sample sizes will allow the ultimate efficiency of making novel discoveries of pathogenic mutations in both mtDNA and the nuclear exome to be determined over time.

While certain of the preferred embodiments of the present invention have been described and specifically exemplified above, it is not intended that the invention be limited to such embodiments. Various modifications may be made thereto without departing from the scope and spirit of the present invention, as set forth in the following claims. 

What is claimed is:
 1. A composition comprising oligonucleotides that specifically hybridize with the nuclear genome and at least one oligonucleotide that specifically hybridizes with mitochondrial DNA, wherein said oligonucleotide that specifically hybridizes with mitochondrial DNA comprises a nucleic acid molecule in FIG.
 6. 2. The composition of claim 1, wherein said oligonucleotides that specifically hybridize with the nuclear genome comprise a whole exome library.
 3. The composition of claim 1, comprising at least 100 of the nucleic acid molecules provided in FIG.
 6. 4. The composition of claim 1, comprising all of the nucleic acid molecules provided in FIG.
 6. 5. The composition of claim 1, wherein said composition comprises oligonucleotides that specifically hybridize with MitoCarta gene sequences.
 6. The composition of claim 5, wherein said composition comprises oligonucleotides that specifically hybridize with at least one gene selected from the group consisting of BCL2, GPX1, LYRM4, MSRB2, NDUFA11, NUDT8, PIGY, PRDX2, PRDX5, SLC25A26, TIMM117B, ZBED5, C6orf136, HSD17B8, MRPS18B, and TAP1.
 7. The composition of claim 1, wherein ratio of oligonucleotides which specifically hybridize with mitochondrial DNA to oligonucleotides which specifically hybridize with the nuclear genome is about 1:75 to about 1:150.
 8. The composition of claim 7, wherein said ratio is about 1:100.
 9. The composition of claim 1, wherein said oligonucleotides are about 20 to about 250 nucleotides in length.
 10. A composition comprising at least one oligonucleotide that specifically hybridizes with mitochondrial DNA, wherein said oligonucleotide comprises a nucleic acid molecule in FIG.
 6. 11. The composition of claim 10, comprising at least 100 of the nucleic acid molecules provided in FIG.
 6. 12. The composition of claim 10, comprising all of the nucleic acid molecules provided in FIG.
 6. 13. The composition of claim 10, wherein said composition comprise oligonucleotides that specifically hybridize with MitoCarta gene sequences.
 14. The composition of claim 13, wherein said composition comprises oligonucleotides that specifically hybridize with at least one gene selected from the group consisting of BCL2, GPX1, LYRM14, MSRB2, NDUFA11, NUDT8, PIGY, PRDX2, PRDX5, SLC25A26, TIMMI17B, ZBED5, C6orf136, HSD17B8, MRPS18B, and TAP1.
 15. A kit comprising the composition of claim
 10. 16. The kit of claim 15, further comprising oligonucleotides that specifically hybridize with the nuclear genome, optionally contained in a separate composition.
 17. A method for detecting genetic mutations associated with a mitochondrial disease, said method comprising a) isolating nucleic acid molecules in a biological sample with at least one oligonucleotide that specifically hybridizes with mitochondrial DNA, wherein said oligonucleotide comprises a nucleic acid molecule in FIG. 6; b) amplifying the isolated nucleic acid molecules, and c) determining the presence or absence of mutation associated with a mitochondrial disease in the amplified DNA. 